Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically ...important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.
A novel sulfated polysaccharide (SCVP-1) was isolated from sea cucumber viscera and purified to elucidate its structure and immune-enhancing ability. SCVP-1 was found to be a homogeneous ...polysaccharide with a relative molecular weight of 180.8 kDa and composed of total sugars (60.2 ± 2.6%), uronic acid (15.3 ± 1.8%), proteins (6.8 ± 0.8%), and sulfate groups (18.1 ± 0.9%). SCVP-1 consisted of mannose, glucosamine, glucuronic acid, N-acetyl-galactosamine, glucose, galactose and fucose at an approximate molar ratio of 1.00:1.41:0.88:2.14:1.90:1.12:1.24. The fourier transform infrared spectra (FT-IR) and nuclear magnetic resonance (NMR) analyses showed that SCVP-1 was a kind of glycosaminoglycan. And the sulfation patterns of the fucose branches were Fuc2,4S, Fuc3,4S and Fuc0S. The surface morphology of SCVP-1 presented loose and irregular sheet structure formed by aggregation of polysaccharide molecules with spherical structure. Moreover, SCVP-1 promoted the production of nitric oxide (NO) and cytokines (IL-1β, IL-6 and TNF-α) by RAW264.7 cells as well as the expression of related genes (iNOS, IL-1β, IL-6 and TNF-α) and also enhanced their phagocytic activity through TLR4-mediated activation of the MAPKs and NF-κB signaling pathways. This study suggests that sea cucumber viscera are good sources of polysaccharides and SCVP-1 might be a novel immunomodulator.
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•First multigene phylogeny that spans extant Holothuroidea.•A revised taxonomy of Holothuroidea is proposed.•Three families are redefined and two new families are ...erected.•Discrepancies between time-tree analyses suggest the need for fossil revision.•Mapping morphology reveals homoplasy but also recovers apomorphies for clades.
Sea cucumbers (Holothuroidea) are a morphologically diverse, ecologically important, and economically valued clade of echinoderms; however, the understanding of the overall systematics of the group remains controversial. Here, we present a phylogeny of extant Holothuroidea assessed with maximum parsimony, maximum likelihood, and Bayesian approaches using approximately 4.3kb of mt- (COI, 16S, 12S) and nDNA (H3, 18S, 28S) sequences from 82 holothuroid terminals representing 23 of the 27 widely-accepted family-ranked taxa. Currently five holothuroid taxa of ordinal rank are accepted. We find that three of the five orders are non-monophyletic, and we revise the taxonomy of the groups accordingly. Apodida is sister to the rest of Holothuroidea, here considered Actinopoda. Within Actinopoda, Elasipodida in part is sister to the remaining Actinopoda. This latter clade, comprising holothuroids with respiratory trees, is now called Pneumonophora. The traditional Aspidochirotida is paraphyletic, with representatives from three orders (Molpadida, Dendrochirotida, and Elasipodida in part) nested within. Therefore, we discontinue the use of Aspidochirotida and instead erect Holothuriida as the sister group to the remaining Pneumonophora, here termed Neoholothuriida. We found four well-supported major clades in Neoholothuriida: Dendrochirotida, Molpadida and two new clades, Synallactida and Persiculida. The mapping of traditionally-used morphological characters in holothuroid systematics onto the phylogeny revealed marked homoplasy in most characters demonstrating that further taxonomic revision of Holothuroidea is required. Two time-tree analyses, one based on calibrations for uncontroversial crown group dates for Eleutherozoa, Echinozoa and Holothuroidea and another using these calibrations plus four more from within Holothuroidea, showed major discrepancies, suggesting that fossils of Holothuroidea may need reassessment in terms of placing these forms with existing crown clades.
•Collagen fibres from sea cucumber were treated by endogenous cysteine proteinases.•Collagen fibrils were disaggregated into collagen fibres by cysteine proteinases.•Cysteine proteinases caused ...increasing structural disorder of collagen fibres.•Cysteine proteinases freed glycosaminoglycan and hydroxyproline.
Autolysis of sea cucumber, caused by endogenous enzymes, leads to postharvest quality deterioration of sea cucumber. However, the effects of endogenous proteinases on structures of collagen fibres, the major biologically relevant substrates in the body wall of sea cucumber, are less clear. Collagen fibres were prepared from the dermis of sea cucumber (Stichopus japonicus), and the structural consequences of degradation of the collagen fibres caused by endogenous cysteine proteinases (ECP) from Stichopus japonicus were examined. Scanning electron microscopic images showed that ECP caused partial disaggregation of collagen fibres into collagen fibrils by disrupting interfibrillar proteoglycan bridges. Differential scanning calorimetry and Fourier transform infrared analysis revealed increased structural disorder of fibrillar collagen caused by ECP. SDS-PAGE and chemical analysis indicated that ECP can liberate glycosaminoglycan, hydroxyproline and collagen fragments from collagen fibres. Thus ECP can cause disintegration of collagen fibres by degrading interfibrillar proteoglycan bridges.
The concentrations of natural radionuclide of super( 238)U and super( 232)Thhave been measured by neutron activation analysis technique in essential vegetables and soil samples collected from farms ...in Cameron Highlands and Penang, Malaysia. The concentrations of natural radionuclide in Tomato, Eggplant, Lattice, Pumpkin, Cucumber, Onion, Okra, and Chilli were measured. In soil, the average concentrations of super( 238)U and super( 232)Thwere 203.83 plus or minus . 2.05 Bq/kg and 186.17 plus or minus 3.35 Bq/kg, respectively in Cameron Highland. The highest concentrations of uranium and thorium were 6.25 plus or minus 1.58 Bq/kg and 2.5 plus or minus 1.55 Bq/kg in cucumber and lettuce products, respectively in the Cameron highlands. The transfer factors of these radionuclides from soil to vegetables were estimated. The highest estimation was in Cucumber and lettuce. These values were compared with the published data and were found to be within acceptable limits.
Prometryn is an occasional triazine herbicide used in aquaculture to kill algae. However, deposition of prometryn at the bottom of the pond poses a potential threat to aquatic animals, especially ...benthos, such as the sea cucumber. This study investigated the toxic effects of prometryn oral exposure on antioxidants, and the intestinal histomorphology and microbiome of sea cucumbers. Results showed that the accumulation of prometryn in the intestine, respiratory tree, and body wall decreased sequentially under the same level. Severe pathological damages were observed in the intestines of sea cucumbers fed with 0.080 and 1.595 g/kg prometryn (measured concentration). Moreover, hydrogen peroxide (H2O2) and malondialdehyde (MDA) concentrations were significantly increased in prometryn treatment groups compared to the control group (P < 0.05), while the catalase (CAT) activity was significantly decreased (P < 0.05) in the coelomic fluid of treatment groups. At the phylum level, the abundance of Proteobacteria was significantly higher in the 0.080 g/kg treatment group than in the control group. In addition, prometryn exposure reduced the diversity of intestinal microflora in sea cucumbers. In conclusion, these results suggest that prometryn has potential toxicity to sea cucumber. Therefore, the harm of prometryn deposited in the sediment to aquatic animals must be a concern in aquaculture.
•The intestine accumulated more prometryn than the respiratory tree and body wall of sea cucumbers by oral exposure.•The toxic effect of prometryn inhibited the antioxidant enzymes of sea cucumbers.•Apostichopus japonicas showed severe pathological damages after exposure to 0.080 and 1.595 g/kg prometryn.•The diversity of intestinal flora was decreased after prometryn exposure.
MicroRNAs (miRNAs) have emerged as key regulators in many pathological processes by suppressing the transcriptional and post-transcriptional expression of target genes. MiR-2008 was previously found ...to be significantly up-regulated in diseased sea cucumber Apostichopus japonicus by high-through sequencing, whereas the reads of miR-137, a well-documented tumor repressor, displayed no significant change. In the present study, we found that miR-137 expression was slightly attenuated and miR-2008 was significantly enhanced after Vibrio splendidus infection or Lipopolysaccharides application. Further target screening and dual-luciferase reporter assay revealed that the two important miRNAs shared a common target gene of betaine-homocysteine S-methyltransferase (AjBHMT), which exhibited noncorrelated messenger RNA and protein expression patterns after bacterial challenge. In order to fully understand their regulatory mechanisms, we conducted the functional experiments in vitro and in vivo. The overexpression of miR-137 in sea cucumber or primary coelomocytes significantly decreased, whereas the inhibition of miR-137 increased the mRNA and protein expression levels of AjBHMT. In contrast, miR-2008 overexpression and inhibition showed no effect on AjBHMT mRNA levels, but the concentration of AjBHMT protein displayed significant changes both in vitro and in vivo. Consistently, the homocysteine (Hcy) contents were also accordingly altered in the aberrant expression analysis of both miRNAs, consistent with the results of the AjBHMT silencing assay in vitro and in vivo. More importantly, small interfering RNA mediated AjBHMT knockdown and Hcy exposure analyses both significantly increased reactive oxygen species (ROS) production and decreased the number of surviving invasive pathogen in sea cucumber coelomocytes. Taken together, these findings confirmed the differential roles of sea cucumber miR-137 and miR-2008 in regulating the common target AjBHMT to promote ROS production and the clearance of pathogenic microorganisms through Hcy accumulation.
•Structure of sea cucumber Acaudina molpadioides fucoidan (Am-FUC) was clarified.•It was deduced from structure of enzymatically prepared low molecular weight Am-FUC.•Am-FUC consists of a novel ...tetrafucose repeating unit with 1→3-linkage.•Am-FUC is distinct from other fucoidans with tetrafucose unit in sulphation pattern.
Structure of fucoidan from sea cucumber Acaudina molpadioides (Am-FUC) was investigated in this study. Low molecular weight polysaccharide of Am-FUC (Am-LMW) was prepared by enzymatic degradation and assayed by nuclear magnetic resonance. According to the structure of Am-LMW, and referring to previously reported information of Am-FUC oligosaccharides, the structure of Am-FUC was elucidated as →3-α-l-Fucp-1→3-α-l-Fucp2,4(OSO3-)-1→3-α-l-Fucp-1→3-α-l-Fucp2(OSO3-)-1→n. Compared to other investigated fucoidans, which also consist of tetrafucose repeating units with 1→3-linkages, Am-FUC contains a novel repeating unit distinctive in sulphation pattern.
This review presents a detailed analysis of published research data focused on the pharmacological activity exerted by biologically active compounds isolated from sea cucumbers belonging to the class ...of Holothuroidea, phylum Echinodermata. The review contains descriptions of the structure, physico-chemical properties and pharmacological effects of these active substances. Particular attention is given to compounds with anticoagulant, antithrombotic, antioxidant, anticancer, anti-infectious, immune-stimulating and anti-ACE (angiotensin converting enzyme) activities as well as to the substances exerting a regulating influence on lipid and carbohydrate metabolism. All these compounds may be considered as prototypes for development of new pharmaceutical substances and medicines.
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